debian/changelog

@@ -7,6 +7,9 @@ hmmer2 (2.5j+dfsg-1) UNRELEASED; urgency=medium
   * New upstream version
   * debhelper 12
   * Standards-Version: 4.3.0
+  * Drop hmmer2-pvm package
+  * libhmmer2-dev package drops static lib (this is not automatically
+    generated by upstream any more)
 
  -- Andreas Tille <tille@debian.org>  Fri, 11 Jan 2019 15:43:07 +0100
 

debian/control

@@ -21,8 +21,7 @@ Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends}
 Recommends: biosquid
-Suggests: hmmer2-doc (>= ${source:Version}),
-          hmmer2-pvm (>= ${binary:Version})
+Suggests: hmmer2-doc (>= ${source:Version})
 Description: profile hidden Markov models for protein sequence analysis
  HMMER is an implementation of profile hidden Markov model methods for
  sensitive searches of biological sequence databases using multiple sequence
@@ -33,24 +32,6 @@ Description: profile hidden Markov models for protein sequence analysis
  a sequence database to find (and/or align) additional homologues of the
  sequence family.
 
-Package: hmmer2-pvm
-Architecture: any
-Depends: ${shlibs:Depends},
-         ${misc:Depends},
-         pvm
-Suggests: hmmer2-doc (>= ${binary:Version})
-Description: HMMER programs with PVM (Parallel Virtual Machine) support
- HMMER is an implementation of profile hidden Markov model methods for
- sensitive searches of biological sequence databases using multiple sequence
- alignments as queries.
- .
- Given a multiple sequence alignment as input, HMMER builds a statistical
- model called a "hidden Markov model" which can then be used as a query into
- a sequence database to find (and/or align) additional homologues of the
- sequence family.
- .
- This package contains HMMER programs compiled with PVM support.
-
 Package: hmmer2-doc
 Architecture: all
 Section: doc

debian/docs

-NOTES

debian/hmmer2-pvm.1

-.TH HMMER-PVM 1 "Tue, 08 Aug 2006 20:00:00 -0300"
-.SH NAME
-hmmer2-pvm \- HMMER utilities for PVM clusters
-.SH DESCRIPTION
-Information on how to use the programs
-.B hmmcalibrate-pvm
-,
-.B hmmpfam-pvm
-and
-.B hmmsearch-pvm
-is available on the section "Configuring a PVM cluster for HMMER" (page 15) at the User's Guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf).
-.PP
-.SH SEE ALSO
-.BR hmmer2 (1),
-.BR hmmer (1)
-.SH AUTHOR
-HMMER was written by Sean Eddy.
-.PP
-This manual page was written by Nelson A. de Oliveira <naoliv@gmail.com>,
-for the Debian project (but may be used by others).

debian/hmmer2-pvm.README.Debian

-hmmer2-pvm for Debian
---------------------
-
- Please, read the section "Configuring a PVM  cluster  for  HMMER"  (page  15)
- at the User's Guide (ftp://selab.janelia.org/pub/software/hmmer/2.3.2/Userguide.pdf), to see how to configure properly Hmmer on a PVM
- cluster.
-
- -- Nelson A. de Oliveira <naoliv@gmail.com>  Tue, 08 Aug 2006 23:07:12 -0300

debian/hmmer2-pvm.install

-debian/tmp/bin/hmm2calibrate-pvm usr/bin
-debian/tmp/bin/hmm2pfam-pvm usr/bin
-debian/tmp/bin/hmm2search-pvm usr/bin

debian/hmmer2-pvm.links

-usr/share/man/man1/hmmer2-pvm.1.gz usr/share/man/man1/hmm2calibrate-pvm.1.gz
-usr/share/man/man1/hmmer2-pvm.1.gz usr/share/man/man1/hmm2pfam-pvm.1.gz
-usr/share/man/man1/hmmer2-pvm.1.gz usr/share/man/man1/hmm2search-pvm.1.gz

debian/hmmer2-pvm.manpages

-debian/hmmer2-pvm.1

debian/hmmer2.docs

+Release-Notes

debian/libhmmer2-dev.install

@@ -4,5 +4,5 @@ src/funcs.h		usr/include/hmmer2
 src/globals.h		usr/include/hmmer2
 src/postprob.h		usr/include/hmmer2
 src/structs.h		usr/include/hmmer2
-src/libhmmer.a		usr/lib/${DEB_HOST_MULTIARCH}
+#src/libhmmer.a		usr/lib/${DEB_HOST_MULTIARCH}
 debian/pkgconfig	usr/lib/${DEB_HOST_MULTIARCH}

debian/patches/fix_install.patch

+Author: Andreas Tille <tille@debian.org>
+Last-Update: Fri, 11 Jan 2019 15:43:07 +0100
+Description: Do not duplicate prefix
+
+--- a/Makefile
++++ b/Makefile
+@@ -55,13 +55,13 @@ src/libhmmer.a:
+ #          Prefix those paths with ${DESTDIR} (rarely used, usually null;
+ #          may be set on a make command line when building contrib RPMs).
+ install:
+-	mkdir -p ${DESTDIR}/$(BINDIR)/
++	mkdir -p $(BINDIR)
+ 
+ 	for file in $(PROGS) ; do\
+-		cp src/$$file "${DESTDIR}/$(BINDIR)/$$file""$(PROGSUFFIX)" ;\
++		cp src/$$file "$(BINDIR)/$$file""$(PROGSUFFIX)" ;\
+ 	done
+ 	for file in hmmer2 $(ls documentation/man/); do\
+-	   install -D documentation/man/$$file.man ${DESTDIR}/$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
++	   install -D documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
+ 	done
+ 
+ # Reverses the steps of "make install".  However, this should be handled

debian/patches/series

 use_debian_packaged_biosquid.patch
 build_libhmmer.a_with-fPIC.patch
 fix_typo.patch
+fix_install.patch

debian/rules

@@ -30,16 +30,13 @@ override_dh_auto_configure:
 override_dh_auto_install:
 	dh_auto_install -- prefix=$(CURDIR)/debian/tmp
 	# lkajan: rename binaries and man pages like this: s/hmm/hmm2/ - except hmmer.1, rename that to hmmer2.1:
-	rename 's/^hmm/hmm2/;' $(CURDIR)/debian/tmp/bin/*
-	cd $(CURDIR)/debian/tmp/bin; rename 's/^hmm/hmm2/;' *
-	cd $(CURDIR)/debian/tmp/share/man/man1; rename 's/^hmm/hmm2/;' *
-	mv $(CURDIR)/debian/tmp/share/man/man1/hmm2er.1 $(CURDIR)/debian/tmp/share/man/man1/hmmer2.1
+	rename 's/^hmm(.+)2/hmm2$$1/;' $(CURDIR)/debian/tmp/bin/*
+	cd $(CURDIR)/debian/tmp/bin; rename 's/^hmm(.+)2/hmm2$$1/;' *
+	cd $(CURDIR)/debian/tmp/share/man/man1; rename 's/^hmm(.+)2/hmm2$$1/;' *
+	# mv $(CURDIR)/debian/tmp/share/man/man1/hmm2er.1 $(CURDIR)/debian/tmp/share/man/man1/hmmer2.1
 	# lkajan: resolve man page hypen issue:
 	sed -i -e 's/--/\\-\\-/g;s/-\([[:alpha:]]\)\b/\\-\1/g;' $(CURDIR)/debian/tmp/share/man/man1/*
 
-override_dh_installchangelogs:
-	dh_installchangelogs -k 00README
-
 override_dh_installexamples:
 	dh_installexamples
 	mkdir -p $(sampledir);